remove redundancy code

JianYang-Lab · Sep 25, 2024 · 631ba7a · 631ba7a
1 parent 719847f
commit 631ba7a
Showing 1 changed file with 2 additions and 6 deletions.
diff --git a/src/gsMap/find_latent_representation.py b/src/gsMap/find_latent_representation.py
@@ -35,23 +35,19 @@ def preprocess_data(adata, params):
 
     sc.pp.filter_genes(adata, min_cells=30)
     if params.data_layer in adata.layers.keys():
+        logger.info(f'Using data layer: {params.data_layer}...')
         adata.X = adata.layers[params.data_layer]
     else:
         raise ValueError(f'Invalid data layer: {params.data_layer}, please check the input data.')
 
     if params.data_layer in ['count', 'counts']:
-
-        adata.X = adata.layers[params.data_layer].copy()
-        # HVGs based on count 
+        # HVGs based on count
         sc.pp.highly_variable_genes(adata,flavor="seurat_v3",n_top_genes=params.feat_cell)
         # Normalize the data
         sc.pp.normalize_total(adata, target_sum=1e4)
         sc.pp.log1p(adata)
 
     elif params.data_layer in adata.layers.keys():
-        logger.info(f'Using {params.data_layer} data...')
-        adata.X = adata.layers[params.data_layer].copy()
-        # HVGs based on normalzied data
         sc.pp.highly_variable_genes(adata,flavor="seurat",n_top_genes=params.feat_cell)
 
     return adata